identifier: traitmech:000385
label: PD-Lambda-5 system
definition: A phage defense system in which an organism possesses a PD-Lambda-5 locus
  represented by DefenseFinder as a two-profile model, PD-Lambda-5__PD-Lambda-5_A
  and PD-Lambda-5__PD-Lambda-5_B, and experimentally linked to T2, T4, T6, LambdaVir,
  SECphi17, SECphi18, SECphi27, T3, and T7 protection when expressed in E. coli.
definition_source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: PD-Lambda-5
  synonym_type: RELATED_SYNONYM
  source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
- synonym_text: PD-Lambda-5__PD-Lambda-5_A
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
- synonym_text: PD-Lambda-5__PD-Lambda-5_B
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
evidence:
- reference: DOI:10.1038/s41564-022-01219-4
  snippet: Here we developed an experimental selection scheme agnostic to genomic
    context to identify defence systems in 71 diverse E. coli strains. Our results
    unveil 21 conserved defence systems, none of which were previously detected as
    enriched in defence islands.
  notes: Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered
    PD-Lambda-5 and related conserved phage-defense systems.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
  snippet: PD-lambda-5 is a two-gene system identified in a P2-like prophage. It encodes
    a protein with a nuclease and a HEPN domain, and a predicted methyltransferase.
    It confers broad anti-phage defense and does not seem to mediate abortive infection.
  notes: The DefenseFinder wiki describes PD-Lambda-5 as a two-gene system from a
    P2-like prophage that can confer broad anti-phage defense.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
  snippet: PD-lambda-5 molecular mechanism has not been described to date.
  notes: The DefenseFinder wiki records the PD-Lambda-5 molecular mechanism as not
    yet described.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
  snippet: 'The PD-Lambda-5 is composed of 2 proteins: PD-Lambda-5_A and PD-Lambda-5_B.'
  notes: The DefenseFinder wiki names PD-Lambda-5 as a two-protein system with PD-Lambda-5_A
    and PD-Lambda-5_B.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
  snippet: The PD-Lambda-5 system in *Plantactinospora sp. BB1* (GCF_003030385.1,
    NZ_CP028159) is composed of 2 proteins PD-Lambda-5_A (WP_159104731.1) PD-Lambda-5_B
    (WP_199853739.1)
  notes: The DefenseFinder wiki illustrates a predicted two-protein PD-Lambda-5 locus
    in RefSeq assembly GCF_003030385.1 on NZ_CP028159.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
  snippet: "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo\
    \ et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>,\
    \ <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia\
    \ coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & SECphi17\
    \ & SECphi18 & SECphi27 & T3 & T7"
  notes: The DefenseFinder experimental-validation diagram links Vassallo et al. to
    an E. coli PD-Lambda-5 source locus expressed in E. coli against T2, T4, T6, LambdaVir,
    SECphi17, SECphi18, SECphi27, T3, and T7.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
  snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n\
    \        LambdaVir\n        SECphi17\n        SECphi18\n        SECphi27\n   \
    \     T3\n        T7"
  notes: The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir,
    SECphi17, SECphi18, SECphi27, T3, and T7 in the PD-Lambda-5 protects-against subgraph.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: PD-Lambda-5 | 10\.1101/2022\.05\.12\.491691 | Mapping the landscape of
    anti-phage defense mechanisms in the E\. coli pangenome
  notes: The DefenseFinder article registry maps the named PD-Lambda-5 system to the
    Vassallo et al. E. coli pangenome phage-defense preprint.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
  snippet: "PD-Lambda-5\tPD-Lambda-5\t2\t2\tPD-Lambda-5__PD-Lambda-5_A, PD-Lambda-5__PD-Lambda-5_B\t\
    \t\t"
  notes: The DefenseFinder rules table models PD-Lambda-5 as a two-profile system
    requiring PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| PD-Lambda-5__PD-Lambda-5_A                       | PD-Lambda-5__PD-Lambda-5_A                       |
    PD-Lambda-5            | Custom                  | 20     |'
  notes: The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_A under
    the PD-Lambda-5 system namespace.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| PD-Lambda-5__PD-Lambda-5_B                       | PD-Lambda-5__PD-Lambda-5_B                       |
    PD-Lambda-5            | Custom                  | 20     |'
  notes: The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_B under
    the PD-Lambda-5 system namespace.
causal_graphs:
- graph_id: pd_lambda_5_locus_restricts_phages
  title: PD-Lambda-5 loci restrict T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27,
    T3, and T7
  description: Conservative system-level sketch linking possession of a PD-Lambda-5
    locus to protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27,
    T3, and T7.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures PD-Lambda-5 as a named DefenseFinder phage-defense
    system while leaving natural host breadth, the direct phage trigger, the effector
    mechanism, and exact PD-Lambda-5 profile-to-protein correspondence unresolved.
  nodes:
  - node_id: pd_lambda_5_locus
    label: PD-Lambda-5 locus
    node_type: GENETIC_ELEMENT
    description: A phage-defense locus represented by the PD-Lambda-5 DefenseFinder
      profiles.
  - node_id: pd_lambda_5_listed_phage_protection
    label: T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 protection
    node_type: BIOLOGICAL_PROCESS
    description: Protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27,
      T3, and T7 by PD-Lambda-5.
  - node_id: pd_lambda_5_system_trait
    label: PD-Lambda-5 system
    node_type: TRAIT
    grounding: traitmech:000385
    description: Possession of a genome-encoded PD-Lambda-5 phage-defense system.
  - node_id: phage_defense_system
    label: phage defense system
    node_type: TRAIT
    grounding: traitmech:000209
    description: Possession of one or more genome-encoded immune systems that inhibit
      bacteriophage infection.
  edges:
  - subject: pd_lambda_5_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: pd_lambda_5_listed_phage_protection
    description: The DefenseFinder wiki links a PD-Lambda-5 locus from Vassallo et
      al. to protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27,
      T3, and T7, and DefenseFinder models PD-Lambda-5 through two mandatory profiles.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
      snippet: PD-lambda-5 is a two-gene system identified in a P2-like prophage.
        It encodes a protein with a nuclease and a HEPN domain, and a predicted methyltransferase.
        It confers broad anti-phage defense and does not seem to mediate abortive
        infection.
      notes: The DefenseFinder wiki describes PD-Lambda-5 as a two-gene system from
        a P2-like prophage that can confer broad anti-phage defense.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
      snippet: 'The PD-Lambda-5 is composed of 2 proteins: PD-Lambda-5_A and PD-Lambda-5_B.'
      notes: The DefenseFinder wiki names PD-Lambda-5 as a two-protein system with
        PD-Lambda-5_A and PD-Lambda-5_B.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
      snippet: "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo\
        \ et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] -->\
        \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2\
        \ & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7"
      notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
        to an E. coli PD-Lambda-5 source locus expressed in E. coli against T2, T4,
        T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
      snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n      \
        \  T6\n        LambdaVir\n        SECphi17\n        SECphi18\n        SECphi27\n\
        \        T3\n        T7"
      notes: The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir,
        SECphi17, SECphi18, SECphi27, T3, and T7 in the PD-Lambda-5 protects-against
        subgraph.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "PD-Lambda-5\tPD-Lambda-5\t2\t2\tPD-Lambda-5__PD-Lambda-5_A, PD-Lambda-5__PD-Lambda-5_B\t\
        \t\t"
      notes: The DefenseFinder rules table models PD-Lambda-5 as a two-profile system
        requiring PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| PD-Lambda-5__PD-Lambda-5_A                       | PD-Lambda-5__PD-Lambda-5_A                       |
        PD-Lambda-5            | Custom                  | 20     |'
      notes: The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_A under
        the PD-Lambda-5 system namespace.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| PD-Lambda-5__PD-Lambda-5_B                       | PD-Lambda-5__PD-Lambda-5_B                       |
        PD-Lambda-5            | Custom                  | 20     |'
      notes: The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_B under
        the PD-Lambda-5 system namespace.
  - subject: pd_lambda_5_listed_phage_protection
    predicate: confers
    predicate_id: METPO:2007700
    object: pd_lambda_5_system_trait
    description: Protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27,
      T3, and T7 realizes the PD-Lambda-5 system trait.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
      snippet: "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo\
        \ et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] -->\
        \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2\
        \ & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7"
      notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
        to an E. coli PD-Lambda-5 source locus expressed in E. coli against T2, T4,
        T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
      snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n      \
        \  T6\n        LambdaVir\n        SECphi17\n        SECphi18\n        SECphi27\n\
        \        T3\n        T7"
      notes: The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir,
        SECphi17, SECphi18, SECphi27, T3, and T7 in the PD-Lambda-5 protects-against
        subgraph.
  - subject: pd_lambda_5_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: PD-Lambda-5 system possession is a phage-defense-system trait.
    evidence:
    - reference: DOI:10.1038/s41564-022-01219-4
      snippet: Here we developed an experimental selection scheme agnostic to genomic
        context to identify defence systems in 71 diverse E. coli strains. Our results
        unveil 21 conserved defence systems, none of which were previously detected
        as enriched in defence islands.
      notes: Vassallo et al. developed the agnostic E. coli pangenome selection that
        uncovered PD-Lambda-5 and related conserved phage-defense systems.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: PD-Lambda-5 | 10\.1101/2022\.05\.12\.491691 | Mapping the landscape
        of anti-phage defense mechanisms in the E\. coli pangenome
      notes: The DefenseFinder article registry maps the named PD-Lambda-5 system
        to the Vassallo et al. E. coli pangenome phage-defense preprint.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "PD-Lambda-5\tPD-Lambda-5\t2\t2\tPD-Lambda-5__PD-Lambda-5_A, PD-Lambda-5__PD-Lambda-5_B\t\
        \t\t"
      notes: The DefenseFinder rules table models PD-Lambda-5 as a two-profile system
        requiring PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B.
discussions:
- discussion_id: pd-lambda-5-mechanism-gap
  prompt: Resolve PD-Lambda-5 natural host breadth, direct phage trigger, effector
    mechanism, and profile-to-protein correspondence before minting narrower PD-Lambda-5
    mechanism traits.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Vassallo et al. support PD-Lambda-5 as one of the conserved systems from
    an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the
    source locus to protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18,
    SECphi27, T3, and T7, and DefenseFinder represents the system with two mandatory
    profiles. Natural host breadth, the direct phage trigger, effector logic, and
    exact profile-to-protein correspondence remain unresolved.
  evidence:
  - reference: DOI:10.1038/s41564-022-01219-4
    snippet: Here we developed an experimental selection scheme agnostic to genomic
      context to identify defence systems in 71 diverse E. coli strains. Our results
      unveil 21 conserved defence systems, none of which were previously detected
      as enriched in defence islands.
    notes: Vassallo et al. developed the agnostic E. coli pangenome selection that
      uncovered PD-Lambda-5 and related conserved phage-defense systems.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
    snippet: PD-lambda-5 is a two-gene system identified in a P2-like prophage. It
      encodes a protein with a nuclease and a HEPN domain, and a predicted methyltransferase.
      It confers broad anti-phage defense and does not seem to mediate abortive infection.
    notes: The DefenseFinder wiki describes PD-Lambda-5 as a two-gene system from
      a P2-like prophage that can confer broad anti-phage defense.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
    snippet: PD-lambda-5 molecular mechanism has not been described to date.
    notes: The DefenseFinder wiki records the PD-Lambda-5 molecular mechanism as not
      yet described.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
    snippet: 'The PD-Lambda-5 is composed of 2 proteins: PD-Lambda-5_A and PD-Lambda-5_B.'
    notes: The DefenseFinder wiki names PD-Lambda-5 as a two-protein system with PD-Lambda-5_A
      and PD-Lambda-5_B.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
    snippet: "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo\
      \ et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>,\
      \ <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] -->\
      \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2\
      \ & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7"
    notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
      to an E. coli PD-Lambda-5 source locus expressed in E. coli against T2, T4,
      T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    snippet: "PD-Lambda-5\tPD-Lambda-5\t2\t2\tPD-Lambda-5__PD-Lambda-5_A, PD-Lambda-5__PD-Lambda-5_B\t\
      \t\t"
    notes: The DefenseFinder rules table models PD-Lambda-5 as a two-profile system
      requiring PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| PD-Lambda-5__PD-Lambda-5_A                       | PD-Lambda-5__PD-Lambda-5_A                       |
      PD-Lambda-5            | Custom                  | 20     |'
    notes: The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_A under
      the PD-Lambda-5 system namespace.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| PD-Lambda-5__PD-Lambda-5_B                       | PD-Lambda-5__PD-Lambda-5_B                       |
      PD-Lambda-5            | Custom                  | 20     |'
    notes: The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_B under
      the PD-Lambda-5 system namespace.
  attaches_to:
  - causal_graphs#pd_lambda_5_locus_restricts_phages
  posed_by: codex
  posed_date: '2026-09-26'
curation_history:
- timestamp: '2026-09-26T14:07:45Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted PD-Lambda-5 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord
    under phage defense system after an ignored-and-hidden duplicate review found
    no exact live TraitMech, METPO, history, or prior proposal record; the replacement
    placeholder is reserved in proposals/metpo_traitmech_v262.
  llm_assisted: true
- timestamp: '2026-09-26T14:07:46Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed PD-Lambda-5 system canonical_examples and left them empty because
    the current sources support an E. coli accession-level experimental validation
    graph, a DefenseFinder system model, and a RefSeq Plantactinospora sp. BB1 example,
    but not a direct native microbial isolate exemplar with experimentally verified
    endogenous PD-Lambda-5 activity. No paid research was used.
  llm_assisted: true